I am trying to perform some composition-based filtering on a large collection of strings (protein sequences).
I wrote a group of three subroutines in order to take care of it, but I'm running into trouble in two ways - one minor, one major. The minor trouble is that when I use List::MoreUtils 'pairwise' I get warnings about using $a and $b only once and them being uninitialized. But I believe I'm calling this method properly (based on CPAN's entry for it and some examples from the web).
The major trouble is an error "Can't use string ("17/32") as HASH ref while "strict refs" in use..."
It seems like this can only happen if the foreach loop in &comp is giving the hash values as a string instead of evaluating the division operation. I'm sure I've made a rookie mistake, but can't find the answer on the web. The first time I even looked at perl code was last Wednesday...
use List::Util;
use List::MoreUtils;
my @alphabet = (
'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I',
'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'
);
my $gapchr = '-';
# Takes a sequence and returns letter = occurrence count pairs as hash.
sub getcounts {
my %counts = ();
foreach my $chr (@alphabet) {
$counts{$chr} = ( $[0] =~ tr/$chr/$chr/ );
}
$counts{'gap'} = ( $[0] =~ tr/$gapchr/$gapchr/ );
return %counts;
}
# Takes a sequence and returns letter = fractional composition pairs as a hash.
sub comp {
my %comp = getcounts( $[0] );
foreach my $chr (@alphabet) {
$comp{$chr} = $comp{$chr} / ( length( $[0] ) - $comp{'gap'} );
}
return %comp;
}
# Takes two sequences and returns a measure of the composition difference between them, as a scalar.
# Originally all on one line but it was unreadable.
sub dcomp {
my @dcomp = pairwise { $a - $b } @{ values( %{ comp( $[0] ) } ) }, @{ values( %{ comp( $[1] ) } ) };
@dcomp = apply { $_ ** 2 } @dcomp;
my $dcomp = sqrt( sum( 0, @dcomp ) ) / 20;
return $dcomp;
}
Much appreciation for any answers or advice!
